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Code Releases Activity

(v2.1.1.9163) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9160
# AMR 2.1.1.9163
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
@ -62,6 +62,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Added Amorolfine (`AMO`, D01AE16), which is now also part of the `antifungals()` selector
* Added Efflux (`EFF`), to allow mapping to AMRFinderPlus
* Added Tigemonam (`TNM`), a monobactam
* Added over 1,500 trade names
* MICs
* Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
* Fixed a bug in `as.mic()` that failed translation of scientifically formatted numbers
@ -76,12 +77,11 @@ This package now supports not only tools for AMR data analysis in clinical setti
* `mo_info()` now contains an extra element `rank` and `group_members` (with the contents of the new `mo_group_members()` function)
* Updated all ATC codes from WHOCC
* Updated all antibiotic DDDs from WHOCC
* Added over 1,500 trade names for antibiotics
* Fix for using a manual value for `mo_transform` in `antibiogram()`
* Fixed a bug for when `antibiogram()` returns an empty data set
* Fix for mapping 'high level' antibiotics in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
* Improved overall algorithm of `as.ab()` for better performance and accuracy, including the new function `as_reset_session()` to remove earlier coercions.
* Improved overall algorithm of `as.mo()` for better performance and accuracy. Specifically:
* Improved overall algorithm of `as.mo()` for better performance and accuracy, specifically:
* More weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species
* Genera from the World Health Organization's (WHO) Priority Pathogen List now have the highest prevalence
* Fixed a bug for `sir_confidence_interval()` when there are no isolates available